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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "gmt music clinical-correlation" .IX Header "gmt music clinical-correlation" .SH "NAME" gmt music clinical\-correlation \- Correlate phenotypic traits against mutated genes, or against individual variants .SH "VERSION" .IX Header "VERSION" This document describes gmt music clinical-correlation version 0.04 (2018\-07\-05 at 09:17:13) .SH "SYNOPSIS" .IX Header "SYNOPSIS" gmt music clinical-correlation \-\-bam\-list=? \-\-output\-file=? [\-\-maf\-file=?] [\-\-glm\-clinical\-data\-file=?] [\-\-use\-maf\-in\-glm] [\-\-skip\-non\-coding] [\-\-skip\-silent] [\-\-clinical\-correlation\-matrix\-file=?] [\-\-input\-clinical\-correlation\-matrix\-file=?] [\-\-genetic\-data\-type=?] [\-\-numeric\-clinical\-data\-file=?] [\-\-numerical\-data\-test\-method=?] [\-\-categorical\-clinical\-data\-file=?] [\-\-glm\-model\-file=?] .PP .Vb 6 \& ... music clinical\-correlation \e \& \-\-bam\-list /path/myBamList.tsv \e \& \-\-maf\-file /path/myMAF.tsv \e \& \-\-numeric\-clinical\-data\-file /path/myNumericData.tsv \e \& \-\-genetic\-data\-type \*(Aqgene\*(Aq \e \& \-\-output\-file /path/output_file \& \& ... music clinical\-correlation \e \& \-\-maf\-file /path/myMAF.tsv \e \& \-\-bam\-list /path/myBamList.tsv \e \& \-\-numeric\-clinical\-data\-file /path/myNumericData.tsv \e \& \-\-categorical\-clinical\-data\-file /path/myClassData.tsv \e \& \-\-genetic\-data\-type \*(Aqgene\*(Aq \e \& \-\-output\-file /path/output_file \& \& ... music clinical\-correlation \e \& \-\-maf\-file /path/myMAF.tsv \e \& \-\-bam\-list /path/myBamList.tsv \e \& \-\-output\-file /path/output_file \e \& \-\-glm\-model\-file /path/model.tsv \e \& \-\-glm\-clinical\-data\-file /path/glm_clinical_data.tsv \e \& \-\-use\-maf\-in\-glm .Ve .SH "REQUIRED ARGUMENTS" .IX Header "REQUIRED ARGUMENTS" .IP "bam-list \fIText\fR" 4 .IX Item "bam-list Text" Tab delimited list of \s-1BAM\s0 files [sample_name, normal_bam, tumor_bam] (See Description) .IP "output-file \fIText\fR" 4 .IX Item "output-file Text" Results of clinical-correlation tool. Will have suffix added for data type .SH "OPTIONAL ARGUMENTS" .IX Header "OPTIONAL ARGUMENTS" .IP "maf-file \fIText\fR" 4 .IX Item "maf-file Text" List of mutations using \s-1TCGA MAF\s0 specification v2.3 .IP "glm-clinical-data-file \fIText\fR" 4 .IX Item "glm-clinical-data-file Text" Clinical traits, mutational profiles, other mixed clinical data (See \s-1DESCRIPTION\s0) .IP "use-maf-in-glm \fIBoolean\fR" 4 .IX Item "use-maf-in-glm Boolean" Create a variant matrix from the \s-1MAF\s0 file as variant input to \s-1GLM\s0 analysis. .Sp Default value 'false' (\-\-nouse\-maf\-in\-glm) if not specified .IP "nouse-maf-in-glm \fIBoolean\fR" 4 .IX Item "nouse-maf-in-glm Boolean" Make use-maf-in-glm 'false' .IP "skip-non-coding \fIBoolean\fR" 4 .IX Item "skip-non-coding Boolean" Skip non-coding mutations from the provided \s-1MAF\s0 file .Sp Default value 'true' if not specified .IP "noskip-non-coding \fIBoolean\fR" 4 .IX Item "noskip-non-coding Boolean" Make skip-non-coding 'false' .IP "skip-silent \fIBoolean\fR" 4 .IX Item "skip-silent Boolean" Skip silent mutations from the provided \s-1MAF\s0 file .Sp Default value 'true' if not specified .IP "noskip-silent \fIBoolean\fR" 4 .IX Item "noskip-silent Boolean" Make skip-silent 'false' .IP "clinical-correlation-matrix-file \fIText\fR" 4 .IX Item "clinical-correlation-matrix-file Text" Specify a file to store the sample-vs-gene matrix created during calculations .IP "input-clinical-correlation-matrix-file \fIText\fR" 4 .IX Item "input-clinical-correlation-matrix-file Text" Instead of creating this from the \s-1MAF,\s0 input the sample-vs-gene matrix for calculations .IP "genetic-data-type \fIText\fR" 4 .IX Item "genetic-data-type Text" Correlate clinical data to \*(L"gene\*(R" or \*(L"variant\*(R" level data .Sp Default value 'gene' if not specified .IP "numeric-clinical-data-file \fIText\fR" 4 .IX Item "numeric-clinical-data-file Text" Table of samples (y) vs. numeric clinical data category (x) .IP "numerical-data-test-method \fIText\fR" 4 .IX Item "numerical-data-test-method Text" Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical clinical data .Sp Default value 'cor' if not specified .IP "categorical-clinical-data-file \fIText\fR" 4 .IX Item "categorical-clinical-data-file Text" Table of samples (y) vs. categorical clinical data category (x) .IP "glm-model-file \fIText\fR" 4 .IX Item "glm-model-file Text" File outlining the type of model, response variable, covariants, etc. for the \s-1GLM\s0 analysis. (See \s-1DESCRIPTION\s0) .SH "DESCRIPTION" .IX Header "DESCRIPTION" This command relates clinical traits and mutational data. Either one can perform correlation analysis between mutations recorded in a \s-1MAF\s0 and the particular phenotypic traits recorded in clinical data files for the same samples, or one can run a generalized linear model (\s-1GLM\s0) analysis on the same types of data. .PP The clinical data files for correlation must be separated between numeric and categoric data and must follow these conventions: .IP "\(bu" 4 Headers are required .IP "\(bu" 4 Each file must include at least 1 sample_id column and 1 attribute column, with the format being [sample_id clinical_data_attribute_1 clinical_data_attribute_2 ...] .IP "\(bu" 4 The sample \s-1ID\s0 must match the sample \s-1ID\s0 listed in the \s-1MAF\s0 under \*(L"Tumor_Sample_Barcode\*(R" for relating the mutations of this sample. .PP Note the importance of the headers: the header for each clinical_data_attribute will appear in the output file to denote relationships with the mutation data from the \s-1MAF.\s0 .PP Internally, the input data is fed into an R script which calculates a P\-value representing the probability that the correlation seen between the mutations in each gene (or variant) and each phenotype trait are random. Lower P\-values indicate lower randomness, or likely true correlations. .PP The results are saved to the output filename given with a suffix appended; \*(L".numeric.csv\*(R" will be appended for results derived from numeric clinical data, and \*(L".categorical.csv\*(R" will be appended for results derived from categorical clinical data. Also, \*(L".glm.csv\*(R" will be appended to the output filename for \s-1GLM\s0 results. .PP The \s-1GLM\s0 analysis accepts a mixed numeric and categoric clinical data file, input using the parameter \-\-glm\-clinical\-data\-file. \s-1GLM\s0 clinical data must adhere to the formats described above for the correlation clinical data files. \s-1GLM\s0 also requires the user to input a \-\-glm\-model\-file. This file requires specific headers and defines the analysis to be performed rather exactly. Here are the conventions required for this file: .IP "\(bu" 4 Columns must be ordered as such: .IP "\(bu" 4 [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ] .IP "\(bu" 4 The 'analysis_type' column must contain either \*(L"Q\*(R", indicating a quantative trait, or \*(L"B\*(R", indicating a binary trait will be examined. .IP "\(bu" 4 The 'clinical_data_trait_name' is the name of a clinical data trait defined by being a header in the \-\-glm\-clinical\-data\-file. .IP "\(bu" 4 The 'variant/gene_name' can either be the name of one or more columns from the \-\-glm\-clinical\-data\-file, or the name of one or more mutated gene names from the \s-1MAF,\s0 separated by \*(L"|\*(R". If this column is left blank, or instead contains \*(L"\s-1NA\*(R",\s0 then each column from either the variant mutation matrix (\-\-use\-maf\-in\-glm) or alternatively the \-\-glm\-clinical\-data\-file is used consecutively as the variant column in independent analyses. .IP "\(bu" 4 \&'covariates' are the names of one or more columns from the \-\-glm\-clinical\-data\-file, separated by \*(L"+\*(R". .IP "\(bu" 4 \&'memo' is any note deemed useful to the user. It will be printed in the output data file for reference. .PP \&\s-1GLM\s0 analysis may be performed using solely the data input into \-\-glm\-clinical\-data\-file, as described above, or alternatively, mutational data from the \s-1MAF\s0 may be included as variants in the \s-1GLM\s0 analysis, as also described above. Use the \-\-use\-maf\-in\-glm flag to include the mutation matrix derived from the maf as variant data. .PP Note that all input files for both correlation and \s-1GLM\s0 analysis must be tab-separated. .SH "ARGUMENTS" .IX Header "ARGUMENTS" .IP "\-\-bam\-list" 4 .IX Item "--bam-list" .RS 4 .PD 0 .IP "Provide a file containing sample names and normal/tumor \s-1BAM\s0 locations for each. Use the tab\- delimited format [sample_name normal_bam tumor_bam] per line. This tool only needs sample_name, so all other columns can be skipped. The sample_name must be the same as the tumor sample names used in the \s-1MAF\s0 file (16th column, with the header Tumor_Sample_Barcode)." 8 .IX Item "Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab- delimited format [sample_name normal_bam tumor_bam] per line. This tool only needs sample_name, so all other columns can be skipped. The sample_name must be the same as the tumor sample names used in the MAF file (16th column, with the header Tumor_Sample_Barcode)." .RE .RS 4 .RE .PD .SH "LICENSE" .IX Header "LICENSE" Copyright (C) 2010\-2011 Washington University in St. Louis. .PP It is released under the Lesser \s-1GNU\s0 Public License (\s-1LGPL\s0) version 3. See the associated \s-1LICENSE\s0 file in this distribution. .SH "AUTHORS" .IX Header "AUTHORS" .Vb 3 \& Nathan D. Dees, Ph.D. \& Qunyuan Zhang, Ph.D. \& William Schierding, M.S. .Ve .SH "SEE ALSO" .IX Header "SEE ALSO" \&\fBgenome-music\fR(1), \fBgenome\fR(1)